Modified or Uncommon Amino Acids

Post Translational Modifications

Terminal Groups

Homoserine lactone: hsl, is produced on the N-terminus after cleavage with CNBr. CNBr selectively cleaves after methionine. The methionine is converted to homoserine lactone.

Target ion m/z

The target ion m/z is used to display only those peptides that are close to the chosen value. The target ion m/z doesn't change the calculations in any way. The value just controls which results are printed.

Isotope Cluster


A given amino acid may be isotopically substituted. The substituted amino acid is assumed to be 100% substituted. Completely unsubstituted and completely substituted amino acid can then be mixed in the specified percentage.


Post-translational modifications:

PIR RESID Database
Rockefeller: PROWL Common Postranslational Modifications
ABRF: Delta Mass. A Database of Protein Post Translational Modifications
ExPASy: Accurate Mass & Pepetide Modification
ExPASy: FindMod tool
ExPASy: Find Mod Tool Masses

Wilkins M.R., Gasteiger E., Gooley A., Herbert B., Molloy M.P., Binz P.A., Ou K., Sanchez J.-C., Bairoch A., Williams K.L, Hochstrasser D.F. High-throughput Mass Spectrometric Discovery of Protein Post-translational Modifications. Journal of Molecular Biology, 289, p. 645-657 (1999).

Wilkins, M.R., Lindskog, I., Gasteiger, E., Bairoch, A., Sanchez, J.-C., Hochstrasser, D.F., and Appel, R.D. Detailed peptide characterisation using PEPTIDEMASS - a World-Wide Web accessible tool. Electrophoresis 18(3-4), 403-408 (1997)

Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.-C., Williams K.L., Appel R.D., Hochstrasser D.F. Protein Identification and Analysis Tools in the ExPASy Server in: 2-D Proteome Analysis Protocols (1998). Editor A.J. Link. Humana Press, New Jersey.

Some Search Engines that include post-translational modifications:

EMBL: Protein & Peptide Group PeptideSearch
UCSF: Protein Prospector
ExPASy: PeptideMass

Stable Isotope Substitution:

S. Sechi, B. T. Chait, "Modification of Cysteine Residues by Alkylation. A Tool in Peptide Mapping and Protein Identification," Anal. Chem., 1998, 70, 5150-5158.

Xian Chen, Z. Fei, L. M. Smith, E. M. Bradbury, V. Majidi, "Stable Isotope Assisted MALDI-TOF Mass Spectrometry for Accurate Determination of Nucleotide Compositions of PCR Products," Anal. Chem., 1999, 71, 3118-3125.